Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01003937.1 Corchorus capsularis cultivar CVL-1 contig03945, whole genome shotgun sequence

Parameters: 2 7 7 80 10 50 1000

Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 957

Length: 1596
ACGTcount: A:0.38, C:0.16, G:0.20, T:0.27


Found at i:34 original size:13 final size:12

Alignment explanation


    Indices: 10--60  Score: 57
    Period size: 13  Copynumber: 3.9  Consensus size: 12

          1 TTTTTTAAA

                         
         10 AAAAATGGTTTTC
          1 AAAAA-GGTTTTC

                          
         23 AGAAAAGGTTTTCC
          1 A-AAAAGGTTTT-C

                *        
         37 AAAATGAGTTTTC
          1 AAAAAG-GTTTTC

                       
         50 AAAAAGGTTTT
          1 AAAAAGGTTTT

         61 TAAGTTTTTT


Statistics
Matches: 33,  Mismatches: 2, Indels: 7
        0.79            0.05        0.17

Matches are distributed among these distances:
  12    5  0.15
  13   17  0.52
  14   11  0.33

ACGTcount: A:0.39, C:0.08, G:0.18, T:0.35


Consensus pattern (12 bp):   
AAAAAGGTTTTC

Found at i:54 original size:14 final size:13

Alignment explanation


    Indices: 10--60  Score: 61
    Period size: 14  Copynumber: 3.9  Consensus size: 13

          1 TTTTTTAAA

                         
         10 AAAAATGGTTTTC
          1 AAAAATGGTTTTC

                          
         23 AGAAAA-GGTTTTC
          1 A-AAAATGGTTTTC

            *             
         36 CAAAATGAGTTTTC
          1 AAAAATG-GTTTTC

                        
         50 AAAAA-GGTTTT
          1 AAAAATGGTTTT

         61 TAAGTTTTTT


Statistics
Matches: 33,  Mismatches: 2, Indels: 7
        0.79            0.05        0.17

Matches are distributed among these distances:
  12    9  0.27
  13   10  0.30
  14   14  0.42

ACGTcount: A:0.39, C:0.08, G:0.18, T:0.35


Consensus pattern (13 bp):   
AAAAATGGTTTTC

Found at i:54 original size:26 final size:26

Alignment explanation


    Indices: 11--60  Score: 84
    Period size: 26  Copynumber: 1.9  Consensus size: 26

          1 TTTTTTAAAA

                                      
         11 AAAATGGTTTTCAGAAAAGGTTTTCC
          1 AAAATGGTTTTCAGAAAAGGTTTTCC

                                     
         37 AAAATGAGTTTTCA-AAAAGGTTTT
          1 AAAATG-GTTTTCAGAAAAGGTTTT

         61 TAAGTTTTTT


Statistics
Matches: 23,  Mismatches: 0, Indels: 2
        0.92            0.00        0.08

Matches are distributed among these distances:
  26   16  0.70
  27    7  0.30

ACGTcount: A:0.38, C:0.08, G:0.18, T:0.36


Consensus pattern (26 bp):   
AAAATGGTTTTCAGAAAAGGTTTTCC
Done.